MolNFT v1 · #15399 · protein

Crystal structure of a human aminoacyl-tRNA synthetase cytokine

1N3L · Tyrosyl-tRNA synthetase: “Crystal structure of a human aminoacyl-tRNA synthetase cytokine”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.72). MolNFT v1 #15399 on GenesisL1: 3D structure, binding sites and…

PDB: 1N3L
Type: protein
Length: 332 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-tRNA synthetase
EC: 6.1.1.1
UniProt: P54577
Ligands: SO4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-tRNA synthetase (EC 6.1.1.1)	protein	332	54% helix, 11% strand	P54577

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	659	0.72	0.79	66	empty
2	56	0.42	0.82	14	empty
3	104	0.40	0.76	14	empty
4	55	0.28	0.74	13	GOL

Compared structures

1N3L · Crystal structure of a human aminoacyl-tRNA synthetase cytokine · the same entry in another collection · chain A against A, TM-score 1.00
P54577 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase, cytoplasmic (P54577) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P54577
Elsewhere: RCSB PDB 1N3L · PDBe 1N3L · UniProt P54577

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